AutoCloner

Multiple sequence alignment - TraesCS4D01G004800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS4D01G004800	chr4D	100.000	1991	0	0	538	2528	2770683	2768693	0.000000e+00	3677
1	TraesCS4D01G004800	chr4D	100.000	207	0	0	1	207	2771220	2771014	1.420000e-102	383
2	TraesCS4D01G004800	chr4B	98.421	1773	18	6	766	2528	2380392	2378620	0.000000e+00	3110
3	TraesCS4D01G004800	chr4B	96.522	230	3	2	538	767	2380776	2380552	2.370000e-100	375
4	TraesCS4D01G004800	chr4B	97.633	169	4	0	39	207	2380989	2380821	8.850000e-75	291
5	TraesCS4D01G004800	chr3D	82.530	498	82	5	1015	1510	33206419	33205925	1.390000e-117	433
6	TraesCS4D01G004800	chr3A	82.129	498	84	5	1015	1510	45708946	45708452	3.010000e-114	422
7	TraesCS4D01G004800	chr3A	89.286	280	29	1	2108	2387	461837541	461837819	1.440000e-92	350
8	TraesCS4D01G004800	chr3B	82.056	496	86	3	1016	1510	55772540	55772047	1.080000e-113	420
9	TraesCS4D01G004800	chr7B	88.333	300	32	3	2093	2391	603826260	603826557	8.600000e-95	357
10	TraesCS4D01G004800	chr5B	87.789	303	31	5	2093	2391	245596371	245596671	1.440000e-92	350
11	TraesCS4D01G004800	chr1A	91.379	174	14	1	2221	2394	239885101	239884929	1.170000e-58	237
12	TraesCS4D01G004800	chr1A	89.394	132	10	3	1	132	440014532	440014405	2.010000e-36	163
13	TraesCS4D01G004800	chr1A	88.636	132	11	3	1	132	551517018	551517145	9.360000e-35	158
14	TraesCS4D01G004800	chr1B	93.182	132	6	1	1	132	621318865	621318993	9.230000e-45	191
15	TraesCS4D01G004800	chr1B	92.366	131	7	1	1	131	621389566	621389693	1.540000e-42	183
16	TraesCS4D01G004800	chr7D	90.152	132	9	2	1	132	564889646	564889519	4.330000e-38	169
17	TraesCS4D01G004800	chr6D	89.394	132	10	2	1	132	25875177	25875050	2.010000e-36	163
18	TraesCS4D01G004800	chr2B	89.394	132	11	1	1	132	737818107	737817979	2.010000e-36	163
19	TraesCS4D01G004800	chr2B	89.394	132	11	1	1	132	737862469	737862597	2.010000e-36	163
20	TraesCS4D01G004800	chrUn	72.584	445	114	8	1070	1510	39290836	39291276	3.390000e-29	139

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS4D01G004800	chr4D	2768693	2771220	2527	True	2030.000000	3677	100.000000	1	2528	2	chr4D.!!$R1	2527
1	TraesCS4D01G004800	chr4B	2378620	2380989	2369	True	1258.666667	3110	97.525333	39	2528	3	chr4B.!!$R1	2489

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
34	35	0.738412	GCACATGTGATTGCCTTGCC	60.738	55.0	29.80	3.51	32.21	4.52	F
1307	1477	0.890683	ACCTACCAAAGCATGCAAGC	59.109	50.0	21.98	5.62	0.00	4.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1457	1627	2.491693	CCGGACACCAAATAGTTTGCAT	59.508	45.455	0.00	0.0	39.31	3.96	R
2500	2672	1.501169	AAAACAAAATCGCTGCTGCC	58.499	45.000	10.24	0.0	35.36	4.85	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
28	29	1.395608	GCATTTGGCACATGTGATTGC	59.604	47.619	29.80	22.08	43.97	3.56
33	34	2.745728	GCACATGTGATTGCCTTGC	58.254	52.632	29.80	6.71	32.21	4.01
34	35	0.738412	GCACATGTGATTGCCTTGCC	60.738	55.000	29.80	3.51	32.21	4.52
35	36	0.892755	CACATGTGATTGCCTTGCCT	59.107	50.000	21.64	0.00	0.00	4.75
36	37	1.274167	CACATGTGATTGCCTTGCCTT	59.726	47.619	21.64	0.00	0.00	4.35
37	38	1.547372	ACATGTGATTGCCTTGCCTTC	59.453	47.619	0.00	0.00	0.00	3.46
80	81	6.346096	TGATCCTATACCAAGTAGTTGCAAC	58.654	40.000	22.17	22.17	31.64	4.17
616	617	8.851145	ACCTACTCAAGAAAAGAAAATCTTTCC	58.149	33.333	5.86	0.00	45.19	3.13
677	678	6.362283	TGAATTACTCGTATATGCATGACACG	59.638	38.462	10.16	15.26	0.00	4.49
1138	1308	0.949397	TACGCCCTACAGATACTGCG	59.051	55.000	0.00	0.00	46.69	5.18
1307	1477	0.890683	ACCTACCAAAGCATGCAAGC	59.109	50.000	21.98	5.62	0.00	4.01
1455	1625	1.153628	CCCCATGTCGGACGAGAAC	60.154	63.158	3.34	0.00	36.56	3.01
1457	1627	0.037697	CCCATGTCGGACGAGAACAA	60.038	55.000	3.34	0.00	36.56	2.83
1875	2045	0.251165	ATCAACCCGTCCCACTTTGG	60.251	55.000	0.00	0.00	37.25	3.28
1888	2058	4.523943	TCCCACTTTGGTTCAAGATGATTG	59.476	41.667	0.00	0.00	35.17	2.67
1952	2122	6.435428	TGAACGAAAAAGCTAAAATCCTGAC	58.565	36.000	0.00	0.00	0.00	3.51
2074	2244	1.777101	CTCTCGCTCCCGATGATTTC	58.223	55.000	0.00	0.00	43.47	2.17
2226	2398	8.544622	TGTTTTGTGGTGACTATAGGATAATCA	58.455	33.333	4.43	0.00	0.00	2.57
2500	2672	3.990092	TGATCCCGATATTTTCTCGTGG	58.010	45.455	0.00	0.00	34.36	4.94
2515	2687	1.444895	GTGGGCAGCAGCGATTTTG	60.445	57.895	0.00	0.00	43.41	2.44

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	1.395608	GCAATCACATGTGCCAAATGC	59.604	47.619	21.38	19.47	41.77	3.56
15	16	0.738412	GGCAAGGCAATCACATGTGC	60.738	55.000	21.38	9.26	40.14	4.57
16	17	0.892755	AGGCAAGGCAATCACATGTG	59.107	50.000	20.18	20.18	0.00	3.21
17	18	1.547372	GAAGGCAAGGCAATCACATGT	59.453	47.619	0.00	0.00	0.00	3.21
18	19	1.822990	AGAAGGCAAGGCAATCACATG	59.177	47.619	0.00	0.00	0.00	3.21
19	20	2.226962	AGAAGGCAAGGCAATCACAT	57.773	45.000	0.00	0.00	0.00	3.21
20	21	1.888512	GAAGAAGGCAAGGCAATCACA	59.111	47.619	0.00	0.00	0.00	3.58
21	22	1.203287	GGAAGAAGGCAAGGCAATCAC	59.797	52.381	0.00	0.00	0.00	3.06
22	23	1.203038	TGGAAGAAGGCAAGGCAATCA	60.203	47.619	0.00	0.00	0.00	2.57
23	24	1.549203	TGGAAGAAGGCAAGGCAATC	58.451	50.000	0.00	0.00	0.00	2.67
24	25	1.829222	CATGGAAGAAGGCAAGGCAAT	59.171	47.619	0.00	0.00	0.00	3.56
25	26	1.203038	TCATGGAAGAAGGCAAGGCAA	60.203	47.619	0.00	0.00	0.00	4.52
26	27	0.405198	TCATGGAAGAAGGCAAGGCA	59.595	50.000	0.00	0.00	0.00	4.75
27	28	0.813821	GTCATGGAAGAAGGCAAGGC	59.186	55.000	0.00	0.00	0.00	4.35
28	29	2.503895	AGTCATGGAAGAAGGCAAGG	57.496	50.000	0.00	0.00	0.00	3.61
29	30	3.822735	TCAAAGTCATGGAAGAAGGCAAG	59.177	43.478	0.00	0.00	0.00	4.01
30	31	3.569701	GTCAAAGTCATGGAAGAAGGCAA	59.430	43.478	0.00	0.00	0.00	4.52
31	32	3.149196	GTCAAAGTCATGGAAGAAGGCA	58.851	45.455	0.00	0.00	0.00	4.75
32	33	3.149196	TGTCAAAGTCATGGAAGAAGGC	58.851	45.455	0.00	0.00	0.00	4.35
33	34	5.772825	TTTGTCAAAGTCATGGAAGAAGG	57.227	39.130	0.00	0.00	0.00	3.46
34	35	6.973843	TCATTTGTCAAAGTCATGGAAGAAG	58.026	36.000	4.03	0.00	0.00	2.85
35	36	6.957920	TCATTTGTCAAAGTCATGGAAGAA	57.042	33.333	4.03	0.00	0.00	2.52
36	37	6.151648	GGATCATTTGTCAAAGTCATGGAAGA	59.848	38.462	4.03	0.00	0.00	2.87
37	38	6.152323	AGGATCATTTGTCAAAGTCATGGAAG	59.848	38.462	4.03	0.00	0.00	3.46
80	81	8.011106	CCAGCTTTTAAACAAACTGCAATATTG	58.989	33.333	11.27	11.27	0.00	1.90
89	90	5.669164	TTGTCCCAGCTTTTAAACAAACT	57.331	34.783	0.00	0.00	0.00	2.66
98	99	4.696455	CTGAACATTTTGTCCCAGCTTTT	58.304	39.130	0.00	0.00	29.14	2.27
677	678	0.038983	AAAACAATTACCGGCCGTGC	60.039	50.000	26.12	0.00	0.00	5.34
749	750	5.018809	ACAACCTATGATGCATGTCCTTTT	58.981	37.500	2.46	0.00	0.00	2.27
750	751	4.400251	CACAACCTATGATGCATGTCCTTT	59.600	41.667	2.46	0.00	0.00	3.11
751	752	3.949754	CACAACCTATGATGCATGTCCTT	59.050	43.478	2.46	0.00	0.00	3.36
752	753	3.548770	CACAACCTATGATGCATGTCCT	58.451	45.455	2.46	0.00	0.00	3.85
809	979	5.245531	TGAACGGATCAGAGCATTAGTTTT	58.754	37.500	0.00	0.00	33.04	2.43
1359	1529	2.688666	TCCCTGAGCTTGGGCGAT	60.689	61.111	17.95	0.00	44.23	4.58
1455	1625	3.919804	CGGACACCAAATAGTTTGCATTG	59.080	43.478	0.00	0.00	39.31	2.82
1457	1627	2.491693	CCGGACACCAAATAGTTTGCAT	59.508	45.455	0.00	0.00	39.31	3.96
1497	1667	3.757248	ATGGCGGGCGATGAGTTCC	62.757	63.158	0.00	0.00	0.00	3.62
1875	2045	7.700505	TGAGCAATATCACAATCATCTTGAAC	58.299	34.615	0.00	0.00	0.00	3.18
1960	2130	3.575256	TGCTTTTGGATCTGTTGCAGAAT	59.425	39.130	2.80	0.00	44.04	2.40
2060	2230	1.943340	GTGAAGGAAATCATCGGGAGC	59.057	52.381	0.00	0.00	0.00	4.70
2286	2458	3.305398	AGTCAGAGAAACCACGTGATC	57.695	47.619	19.30	12.21	0.00	2.92
2461	2633	3.935818	TCAACCTCTGGTAACCACAAA	57.064	42.857	0.00	0.00	33.12	2.83
2500	2672	1.501169	AAAACAAAATCGCTGCTGCC	58.499	45.000	10.24	0.00	35.36	4.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.